You could use a crontab. Personal preference is to write a custom script to be called by cron and execute it so as to write a log file also in the process.
#! /bin/bash
scantime=$(date -u +%H)
#writes hour of scan, assuming to be run every 6 hours
fileout="$HOME/clamav-$(date -u +'%Hh-%d-%Y').log"
path="/var $HOME/Downloads"
for i in $path; do
echo "Starting hourly scan of $i
clamscan -r --bell -i $i >> $fileout
wait
done
and then add `0 0 0/6 1/1 * ? * /path/to/script` to `crontab -e`. This will run the script every 6 hours.